VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Mar 26 2007 - 16:33:51 CDT

On Mon, 26 Mar 2007, Jianhui Tian wrote:

JT> hi all,
JT>
JT> I am writing a short script to calculate the End-to-End distance for a
JT> protein molecule. I have two dcd files to analysis together. But I
JT> find that I have difficulty to add the second dcd trajectory file. The
JT> beginning of the script is like following:
JT>
JT>
JT> ##########################
JT> set dcdFile1 n_aka3rm14w6_run10.dcd ;# name of your psf file
JT> set dcdFile2 n_aka3rm14w6_run11.dcd
JT>
JT> set parm aka3rm14w6.prmtop ;# name of parm file
JT>
JT> set incrm 1
JT> ##########################
JT> mol load parm7 $parm dcd $dcdFile1
JT> mol addfile $dcdFile2
JT>
JT> set num_steps [molinfo top get numframes]
JT> .
JT> .
JT> .
JT>
JT> The "mol addfile $dcdFile2" command only added the first three frames
JT> to the top molecule. How to solve the problem? Thanks a lot in
JT> advance.

please add a 'waitfor all' at the and of the mol load and mol addfile.
for details see the scripting section of the vmd users manual.

cheers,
   axel.

JT>
JT> Jianhui
JT> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.